Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

Hi, On Thu, Oct 1, 2015 at 6:30 PM Szilárd Páll wrote: > On Thu, Oct 1, 2015 at 8:01 AM, Venkat Reddy wrote: > > Gromacs-5.1 version can not read xtc files. However, it can access single > > frame gro/pdb files. > > > > That's a bold claim that IMO requires equally strong proof. > I agree with

Re: [gmx-users] distance dependent energy

Thank you Mark and Erik, Van On Wednesday, 23 September 2015, Mark Abraham wrote: > Hi, > > On Tue, Sep 22, 2015 at 5:47 PM Cuong Nguyen > wrote: > > > Dear Gromacs users, > > > > I would like to work out the energy (total and kinetic) as a function of > > the distance from the center of mass o

[gmx-users] vdw modifier and coulomb modifier

Dear all, What does vdw and coulomb modifier do in simulation?. Does these option affect simulation accuracy. I did not find these term in literature or any book, why did gromacs introduce these option? Thanks Masrul -- Gromacs Users mailing list * Please search the archive at http://www.groma

[gmx-users] Free Energy of Liquid Water

Hi everyone, I would like to use Gromacs to do Thermodynamic Integration (TI) from liquid water (TIP4P model) to an ideal gas, to find the relative free energy. To do this, I believe one generally integrates above the critical point by increasing the temperature above the critical temperature

[gmx-users] Query regarding exclusions and Coulomb-SR energies

Dear all, As the Verlet cut-off scheme does not support energygrp-excl parameter yet, we are looking for an alternative to exclude all non bonded interactions between the frozen atoms. The gromacs manual (section 5.4) states that all the non bonded interactions between the pairs in the [ exclusio

[gmx-users] GMXLIB does not induce residuetype.dat

Dear list, I have my own force field working folder so I cloned the entire top folder to no mess with the original files. I added residues to the residue type file to add my residues to the protein group. My FF is included due to the GMXLIB environmental variable but my modified residuestype.da

Re: [gmx-users] Install Gromacs on VirtualBox

I used this: > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=OFF > -DGMX_USE_RDTSCP=OFF But Still: Test project /home/simon/gromacs-5.0.6/build Start 1: TestUtilsUnitTests 1/15 Test #1: TestUtilsUnitTests ...***Exception: Illegal 0.29 sec Start 2: Prepr

[gmx-users] Query regarding exclusions and Coulomb-SR energies

Dear all, As the Verlet cut-off scheme does not support energygrp-excl parameter yet, we are looking for an alternative to exclude all non bonded interactions between the frozen atoms. The gromacs manual (section 5.4) states that all the non bonded interactions between the pairs in the [ exclusio

Re: [gmx-users] Peptide, lipid simulation

On 10/1/15 9:07 AM, badamkhatan togoldor wrote: Dear Gromacs Users,I would like to use g_membed to insert my peptide into membrane. But I got this errors and notes in grompp ERROR 1 [file membed.mdp]: Energy group exclusions are not (yet) implemented for the Verlet scheme NOTE 4 [file memb

Re: [gmx-users] frequent stop of GPU jobs at specific simulation steps.

TL; DR If you want to investigate the issue further check my reply here: http://comments.gmane.org/gmane.science.biology.gromacs.user/80120 -- Szilárd On Mon, Sep 28, 2015 at 5:34 AM, Zhongjin He wrote: > Dear GMX users, > > > Recently I encountered a strange problem in using GPU GROMACS 5.0.6

Re: [gmx-users] Martini domain decomposition problem

Hi Gábor, Without more details (and little experience with martini systems) I can suggest: tweaking DD so you don't end up with a too small box wrt the number of cells by: - Changing the number of ranks by using less/more cores to get a convenient decomposition; I assume you had 6x4x4 before on 96

Re: [gmx-users] GPU+CPU

On Sun, Sep 20, 2015 at 7:11 PM, Parker de Waal wrote: > Hello Everyone, > > I recently started to explore GROMACS (switching over from AMBER) and need > some help understanding how to launch GPU+CPU simulations. > > GROMACS 5.0.6 was compiled with the following cmake arguments: > cmake .. -DGMX_

Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

On Thu, Oct 1, 2015 at 8:01 AM, Venkat Reddy wrote: > Hi > Gromacs-5.1 version can not read xtc files. However, it can access single > frame gro/pdb files. > That's a bold claim that IMO requires equally strong proof. In your other mail to the list you were talking about a 32-bit Ubuntu VM. Are

Re: [gmx-users] polymer in octahedron box pbc problem

Hi, I think its solved, I used -center option but now rather selecting full polymer I selected some of the central residue in polymer chain. Now box looks good and polymer is not broken. JIom On Thu, Oct 1, 2015 at 3:43 PM, gromacs query wrote: > Hi Victor, > > With 'pbc whole' polymer remains

Re: [gmx-users] Install Gromacs on VirtualBox

My guess is that you need to turn off RDTSCP: http://www.gromacs.org/Documentation/Installation_Instructions_5.0#portability-aspects -- Szilárd On Thu, Oct 1, 2015 at 4:36 PM, Simon Dürr wrote: > I have problems installing Gromacs on a VirtualBox machine. > > Stats of the System: > Lubuntu 32

Re: [gmx-users] polymer in octahedron box pbc problem

Hi Victor, With 'pbc whole' polymer remains broken in pbc and the octahedron box looks weird too. JIom On Thu, Oct 1, 2015 at 2:52 PM, Victor Rosas Garcia wrote: > Have you tried the option "-pbc whole" instead of "-pbc mol"? > > Victor > > 2015-10-01 6:43 GMT-05:00 gromacs query : > > > Hi Al

[gmx-users] Install Gromacs on VirtualBox

I have problems installing Gromacs on a VirtualBox machine. Stats of the System: Lubuntu 32bit, 14.04 LTS build-essential and cmake are installed. I follow the instructions: > tar xfz gromacs-5.0.6.tar.gz > cd gromacs-5.0.6 > mkdir build > cd build > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONT

Re: [gmx-users] Error in gromacs-5.1 installation

Hi, Can you please open an issue on redmine.gromacs.org and attach your CMakeCache.txt file to the issue. To work around the issue, you'll likely have to disable NVML support which ATM requires removing all lines that start with "NVML_" from your CMakeCache file. Cheers, -- Szilárd On Tue, Sep

Re: [gmx-users] Gromacs GPU got hang

The only way to know more is to either attach a debugger to the hanging process or possibly with an ltrace/strace to see in which library or syscalls is the process hanging. I suggest you try attaching a debugger and getting a stack trace (see https://sourceware.org/gdb/onlinedocs/gdb/Attach.html)

Re: [gmx-users] How OpenMP works with CUDA/GPU in Gromacs

Hi, I suggest you check some of our recent papers on the heterogeneous parallelization. Chapter two in the following (GROMACS 4.6-related) paper gives a good overview of the (then) new parallelization aspects like threading and GPU acceleration: http://link.springer.com/chapter/10.1007/978-3-319-

Re: [gmx-users] please help in analysis of picture attached

this list does not accept attachments. Please upload your file to some file-sharing service and tell us the link. Victot 2015-10-01 2:21 GMT-05:00 surbhi mahajan : > Hi, > I am trying to do simulations using lipids like DPPC and DMPC , i am not > able to develop a coarse grained model nor am i

Re: [gmx-users] polymer in octahedron box pbc problem

Have you tried the option "-pbc whole" instead of "-pbc mol"? Victor 2015-10-01 6:43 GMT-05:00 gromacs query : > Hi All, > > I have linear polymer in octahedron box and when I try to visualise a > polymer in octahedraon box then water octahedron box looks as expected but > my polymer looks broke

[gmx-users] Peptide, lipid simulation

Dear Gromacs Users,I would like to use g_membed to insert my peptide into membrane. But I got this errors and notes in grompp ERROR 1 [file membed.mdp]:   Energy group exclusions are not (yet) implemented for the Verlet scheme NOTE 4 [file membed.mdp]:   NVE simulation with an initial temperature

Re: [gmx-users] colleague subscribed to gromacs mailing list but unable to get replies

On 01/10/15 09:09, Raag Saluja wrote: Hi! A colleague of mine is having a little problem with the gromacs mailing list. She says she subscribed to it, but when she posts, she gets no reply. She does get the digest, however. She asked me to ask you if you could kindly help her. Have her go to

Re: [gmx-users] colleague subscribed to gromacs mailing list but unable to get replies

On 10/1/15 3:09 AM, Raag Saluja wrote: Hi! A colleague of mine is having a little problem with the gromacs mailing list. She says she subscribed to it, but when she posts, she gets no reply. She does get the digest, however. She asked me to ask you if you could kindly help her. Use the web

Re: [gmx-users] Atom OXT in PHE

On 9/30/15 1:06 PM, Sepideh Kavousi wrote: Hi, In the force fiels that you use this atom in not introduced. you have to import the information of atom in the atomtypes.atp file in the related force field you use The error is not at all related to the content of atomtypes.atp. The problem is

Re: [gmx-users] Insert molecules in system with minimum distance between them

On 9/30/15 12:15 PM, Ebert Maximilian wrote: Dear list, I am trying to add n-number of molecules in my prepare protein+water+ions box but keep a minimum distance of 1 nm in all directions between the newly inserted molecules. On top of that I want to replace solvent molecules with the newly

[gmx-users] polymer in octahedron box pbc problem

Hi All, I have linear polymer in octahedron box and when I try to visualise a polymer in octahedraon box then water octahedron box looks as expected but my polymer looks broken. trjconv_avx -f input.xtc -o out.xtc -pbc mol -ur compact -s input.tpr -b 10 I have tried to use -center (whole po

[gmx-users] protein simulation

Dear GMX users i want to compare binding free energy between experimental and MD computations In experimental methods, we assumed that all atoms of a protein that binding to ligand, butin MD simulations, we just assume the sections of subdomain(s) that binds to ligand Is this way correct to compar

Re: [gmx-users] Simulations of proteins in membrane bilayer

Hey, If that doesn't do the trick use the flags suggested by Terry and also '-ur compact'. This works for me. Regards, On 1 October 2015 at 02:49, Terry wrote: > Hi, > > Try options '-pbc mol -center' with the gmx trjconv tool. > > Terry > > > On Thu, Oct 1, 2015 at 4:48 AM, 凌未风 wrote: > > >

[gmx-users] please help in analysis of picture attached

Hi, I am trying to do simulations using lipids like DPPC and DMPC , i am not able to develop a coarse grained model nor am i able to understand the purpose of the bead that i have got from SBCG model . Please help me in analyzing this attachment. I am very new to this field. please help Regards Su

[gmx-users] colleague subscribed to gromacs mailing list but unable to get replies

Hi! A colleague of mine is having a little problem with the gromacs mailing list. She says she subscribed to it, but when she posts, she gets no reply. She does get the digest, however. She asked me to ask you if you could kindly help her. -- Regards, Raag -- Gromacs Users mailing list * Plea